Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005737 cytoplasm	IBA GO_REF:0000033	ACCEPT	Summary: APIP is localized to the cytoplasm. Immunofluorescence studies showed "APIP was detected mainly in the cytoplasm of HeLa cells" (PMID:23285211). The IBA annotation from phylogenetic inference is consistent with experimental evidence. Reason: Cytoplasmic localization is well-supported by immunofluorescence data (PMID:23285211) and is consistent with its role in the cytosolic methionine salvage pathway. Supporting Evidence: PMID:23285211 In accordance with its putative role in the methionine salvage pathway, APIP was detected mainly in the cytoplasm of HeLa cells by immunofluorescence
GO:0019509 L-methionine salvage from methylthioadenosine	IBA GO_REF:0000033	ACCEPT	Summary: APIP functions as MtnB in the methionine salvage pathway. This is its primary enzymatic function. Knockdown studies showed that "APIP depletion specifically impaired the capacity of cells to grow" when methionine was replaced by MTA (PMID:23285211). Ko et al. (2012) confirmed "The role of APIP in methionine salvage was confirmed by growth assays with methionine-deficient media and quantitation of the methionine salvage substrate, 5'-methylthioadenosine" (PMID:22837397). Reason: This represents the core evolved function of APIP. Multiple studies demonstrate APIP's essential role in the methionine salvage pathway through functional assays. Supporting Evidence: PMID:23285211 We show that APIP depletion specifically impaired the capacity of cells to grow PMID:22837397 The role of APIP in methionine salvage was confirmed by growth assays with methionine-deficient media and quantitation of the methionine salvage substrate, 5'-methylthioadenosine
GO:0046570 methylthioribulose 1-phosphate dehydratase activity	IBA GO_REF:0000033	ACCEPT	Summary: APIP catalyzes the dehydration of MTRu-1-P with measured kinetic parameters of Km ~9.32 uM and Vmax ~1.39 umol/min/mg (PMID:24367089). The crystal structure at 2.0 A resolution (PDB 4M6R) confirms a class II aldolase fold with active-site zinc. This is the core molecular function of APIP. Reason: This is the primary molecular function of APIP, well-characterized structurally and biochemically. Supporting Evidence: PMID:24367089 Here we report the structural and enzymatic characterization of human APIP as an MtnB enzyme with a Km of 9.32 μM and a Vmax of 1.39 μmol min(-1) mg(-1)
GO:0005737 cytoplasm	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation for cytoplasm based on InterPro domains and UniProt subcellular location data. Consistent with experimental IDA evidence from PMID:23285211. Reason: Consistent with experimental evidence; duplicates IBA and IDA annotations but this is acceptable as it represents an independent computational prediction that agrees with experimental data. Supporting Evidence: PMID:23285211 APIP was detected mainly in the cytoplasm of HeLa cells by immunofluorescence
GO:0006915 apoptotic process	IEA GO_REF:0000043	MARK AS OVER ANNOTATED	Summary: This annotation is an OVER-ANNOTATION. APIP does not participate in apoptosis - it INHIBITS apoptosis as a moonlighting function separate from its enzymatic activity. Kang et al. (2014) demonstrated that "APIP/MtnB functions as a cell death inhibitor independently of its MtnB enzyme activity for apoptosis induced by either hypoxia or etoposide" (PMID:24367089). The gene was named "APAF1-interacting protein" because it binds Apaf-1 CARD and competes with procaspase-9, thereby inhibiting apoptosome formation. GO:0006915 (apoptotic process) implies direct participation in apoptosis, which is inappropriate for an inhibitor. Reason: APIP is an INHIBITOR of apoptosis, not a participant. The IEA mapping from UniProt keyword "Apoptosis" does not distinguish between proteins that participate in apoptosis and those that regulate/inhibit it. The proper annotation would be GO:0043066 (negative regulation of apoptotic process), which is already annotated with IMP evidence. Supporting Evidence: PMID:24367089 APIP/MtnB functions as a cell death inhibitor independently of its MtnB enzyme activity for apoptosis induced by either hypoxia or etoposide PMID:24367089 APIP, Apaf-1 interacting protein, has been known to inhibit two main types of programmed cell death, apoptosis and pyroptosis file:human/APIP/APIP-deep-research-falcon.md APIP competes with procaspase-9 for Apaf-1 binding, inhibiting apoptosome-driven caspase-9 activation and offering cytoprotection in hypoxia/ischemia models
GO:0008270 zinc ion binding	IEA GO_REF:0000104	ACCEPT	Summary: APIP is a zinc-dependent enzyme. The crystal structure (PDB 4M6R) shows zinc coordination by His115, His117, and His195 (PMID:24367089). UniProt notes "Binds 1 zinc ion per subunit." IEA is consistent with IDA evidence. Reason: Zinc binding is essential for catalytic activity and is demonstrated in the crystal structure. The IEA annotation is consistent with experimental IDA evidence. Supporting Evidence: PMID:24367089 an overall fold similar to members of the zinc-dependent class II aldolase family
GO:0008652 amino acid biosynthetic process	IEA GO_REF:0000043	ACCEPT	Summary: The methionine salvage pathway regenerates methionine from 5'-methylthioadenosine. While technically methionine biosynthesis, GO:0019509 (L-methionine salvage from methylthioadenosine) is more specific and appropriate. This general term is acceptable but less informative. Reason: APIP does participate in amino acid biosynthesis (methionine salvage), though the more specific term GO:0019509 is preferred and already annotated. Supporting Evidence: PMID:23285211 these results confirm the involvement of APIP in the methionine salvage pathway
GO:0016829 lyase activity	IEA GO_REF:0000043	ACCEPT	Summary: APIP has EC 4.2.1.109 (lyase activity). The more specific term GO:0046570 (methylthioribulose 1-phosphate dehydratase activity) is already annotated with IDA evidence. This general lyase annotation is acceptable but less informative. Reason: APIP is indeed a lyase (EC 4.2.1.109). The annotation is correct but the more specific GO:0046570 is preferred and already present. Supporting Evidence: PMID:24367089 5-methylthioribulose-1-phosphate dehydratase, or MtnB, in the methionine salvage pathway
GO:0019509 L-methionine salvage from methylthioadenosine	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation for methionine salvage based on InterPro domains. Consistent with IBA and IMP evidence for this annotation. Reason: This is the core biological process for APIP. The IEA annotation from domain analysis agrees with experimental evidence. Supporting Evidence: PMID:23285211 these results confirm the involvement of APIP in the methionine salvage pathway
GO:0046570 methylthioribulose 1-phosphate dehydratase activity	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation for the dehydratase activity based on Rhea reaction mapping (EC:4.2.1.109). Consistent with IDA evidence from PMID:24367089. Reason: This is the core molecular function of APIP. The computational annotation agrees with direct enzyme assay data. Supporting Evidence: PMID:24367089 Here we report the structural and enzymatic characterization of human APIP as an MtnB enzyme with a Km of 9.32 μM and a Vmax of 1.39 μmol min(-1) mg(-1)
GO:0046872 metal ion binding	IEA GO_REF:0000120	ACCEPT	Summary: APIP binds zinc as a cofactor. The more specific GO:0008270 (zinc ion binding) is already annotated. This general metal ion binding annotation is correct but less informative. Reason: APIP binds zinc ions. The annotation is correct, though the more specific zinc ion binding term is preferred. Supporting Evidence: PMID:24367089 zinc-dependent class II aldolase family
GO:0005515 protein binding	IPI PMID:16189514 Towards a proteome-scale map of the human protein-protein in...	REMOVE	Summary: High-throughput protein-protein interaction study. "Protein binding" is uninformative and should generally be avoided per curation guidelines. Reason: "Protein binding" does not tell us about the actual function of APIP. The interaction detected is likely part of high-throughput screening and does not represent a specific functional interaction. More informative terms like "identical protein binding" for homomeric interactions are preferred. Supporting Evidence: PMID:16189514 Towards a proteome-scale map of the human protein-protein interaction network.
GO:0005515 protein binding	IPI PMID:19060904 An empirical framework for binary interactome mapping.	REMOVE	Summary: High-throughput interactome mapping study. Uninformative term. Reason: "Protein binding" is too vague and uninformative about APIP's actual function. Supporting Evidence: PMID:19060904 An empirical framework for binary interactome mapping.
GO:0005515 protein binding	IPI PMID:25416956 A proteome-scale map of the human interactome network.	REMOVE	Summary: Proteome-scale interactome mapping. Generic protein binding annotation. Reason: "Protein binding" is uninformative. High-throughput interaction data should be represented by more specific binding terms where possible. Supporting Evidence: PMID:25416956 A proteome-scale map of the human interactome network.
GO:0005515 protein binding	IPI PMID:27107014 An inter-species protein-protein interaction network across ...	REMOVE	Summary: Inter-species protein-protein interaction study. Generic annotation. Reason: Uninformative term from high-throughput study. Supporting Evidence: PMID:27107014 An inter-species protein-protein interaction network across vast evolutionary distance.
GO:0005515 protein binding	IPI PMID:29892012 An interactome perturbation framework prioritizes damaging m...	REMOVE	Summary: High-throughput interactome perturbation study. Generic annotation. Reason: Uninformative term. Supporting Evidence: PMID:29892012 Jun 11. An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders.
GO:0005515 protein binding	IPI PMID:31515488 Extensive disruption of protein interactions by genetic vari...	REMOVE	Summary: Study on genetic variants affecting protein interactions. Generic annotation. Reason: Uninformative term from high-throughput study. Supporting Evidence: PMID:31515488 Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.
GO:0005515 protein binding	IPI PMID:32296183 A reference map of the human binary protein interactome.	REMOVE	Summary: Reference map of human binary interactome. Generic protein binding annotation. Reason: Uninformative. The identical protein binding annotation (GO:0042802) from the same reference is more informative. Supporting Evidence: PMID:32296183 Apr 8. A reference map of the human binary protein interactome.
GO:0005515 protein binding	IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ...	REMOVE	Summary: Interactome mapping for neurodegenerative disease proteins. Generic annotation. Reason: Uninformative term. Supporting Evidence: PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
GO:0005515 protein binding	IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling...	REMOVE	Summary: Dual proteome-scale networks study. Generic protein binding annotation. Reason: Uninformative term from high-throughput study. Supporting Evidence: PMID:33961781 2021 May 6. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
GO:0042802 identical protein binding	IPI PMID:16189514 Towards a proteome-scale map of the human protein-protein in...	ACCEPT	Summary: APIP forms homotetramers. The crystal structure (PDB 4M6R) shows "APIP/MtnB exists as a tetramer in solution and exhibits an assembly with C4 symmetry" (PMID:24367089). Identical protein binding is appropriate for homooligomeric proteins. Reason: APIP is a homotetramer, and self-interaction is required for its enzymatic function. The annotation accurately reflects the protein's quaternary structure. Supporting Evidence: PMID:24367089 APIP/MtnB exists as a tetramer in solution and exhibits an assembly with C4 symmetry in the crystal lattice PMID:16189514 Towards a proteome-scale map of the human protein-protein interaction network.
GO:0042802 identical protein binding	IPI PMID:19060904 An empirical framework for binary interactome mapping.	ACCEPT	Summary: Duplicate annotation for APIP homotetrameric assembly. Same rationale as above. Reason: Consistent with structural evidence for homotetramer formation. Supporting Evidence: PMID:24367089 APIP/MtnB exists as a tetramer in solution PMID:19060904 An empirical framework for binary interactome mapping.
GO:0042802 identical protein binding	IPI PMID:25416956 A proteome-scale map of the human interactome network.	ACCEPT	Summary: Additional evidence for APIP self-interaction/homotetramer formation. Reason: Consistent with structural and biochemical evidence. Supporting Evidence: PMID:24367089 APIP/MtnB exists as a tetramer in solution PMID:25416956 A proteome-scale map of the human interactome network.
GO:0042802 identical protein binding	IPI PMID:31515488 Extensive disruption of protein interactions by genetic vari...	ACCEPT	Summary: APIP self-interaction detected in genetic variant study. Reason: Consistent with known homotetrameric structure. Supporting Evidence: PMID:24367089 APIP/MtnB exists as a tetramer in solution PMID:31515488 Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.
GO:0042802 identical protein binding	IPI PMID:32296183 A reference map of the human binary protein interactome.	ACCEPT	Summary: APIP self-interaction in binary interactome reference map. Reason: Consistent with known homotetrameric structure. Supporting Evidence: PMID:24367089 APIP/MtnB exists as a tetramer in solution PMID:32296183 Apr 8. A reference map of the human binary protein interactome.
GO:0070372 regulation of ERK1 and ERK2 cascade	IEA GO_REF:0000107	UNDECIDED	Summary: Transferred from mouse ortholog. The evidence for APIP involvement in ERK1/2 cascade regulation is weak and may not represent a core function. Reason: Unable to access primary literature for the mouse ortholog annotation to evaluate the strength of evidence. This may represent a peripheral or context-dependent effect rather than a core function.
GO:0005737 cytoplasm	IDA PMID:23285211 Functional identification of APIP as human mtnB, a key enzym...	ACCEPT	Summary: Direct experimental evidence for cytoplasmic localization by immunofluorescence. "APIP was detected mainly in the cytoplasm of HeLa cells" (PMID:23285211). Reason: Strong experimental evidence for cytoplasmic localization, consistent with its role in the cytosolic methionine salvage pathway. Supporting Evidence: PMID:23285211 In accordance with its putative role in the methionine salvage pathway, APIP was detected mainly in the cytoplasm of HeLa cells by immunofluorescence
GO:0008270 zinc ion binding	IDA PMID:24367089 Structural and biochemical basis for the inhibition of cell ...	ACCEPT	Summary: Crystal structure at 2.0 A resolution (PDB 4M6R) directly demonstrates zinc binding at the active site. His115, His117, and His195 coordinate the zinc ion. Reason: High-resolution structural data directly demonstrates zinc binding, which is essential for catalytic activity. Supporting Evidence: PMID:24367089 The crystal structure was determined at 2.0-Å resolution, revealing an overall fold similar to members of the zinc-dependent class II aldolase family
GO:0043066 negative regulation of apoptotic process	IMP PMID:24367089 Structural and biochemical basis for the inhibition of cell ...	KEEP AS NON CORE	Summary: APIP inhibits caspase-9-dependent apoptosis by binding to Apaf-1 CARD and competing with procaspase-9 for apoptosome formation. Importantly, "APIP/MtnB functions as a cell death inhibitor independently of its MtnB enzyme activity for apoptosis" (PMID:24367089). This is a moonlighting function. Reason: This is a well-documented moonlighting function of APIP that is INDEPENDENT of its enzymatic activity. It represents a secondary regulatory role rather than the primary evolved function. The anti-apoptotic effect requires physical binding to Apaf-1 but not dehydratase activity. Supporting Evidence: PMID:24367089 APIP/MtnB functions as a cell death inhibitor independently of its MtnB enzyme activity for apoptosis induced by either hypoxia or etoposide PMID:24367089 APIP, Apaf-1 interacting protein, has been known to inhibit two main types of programmed cell death, apoptosis and pyroptosis
GO:0046570 methylthioribulose 1-phosphate dehydratase activity	IDA PMID:24367089 Structural and biochemical basis for the inhibition of cell ...	ACCEPT	Summary: Direct enzyme assay demonstrated dehydratase activity with Km = 9.32 uM and Vmax = 1.39 umol/min/mg. Mutational analysis confirmed active site residues (Q96A, C97A, H115A, E139A affect activity). Reason: This is the core molecular function of APIP, demonstrated by direct biochemical characterization with kinetic parameters. Supporting Evidence: PMID:24367089 Here we report the structural and enzymatic characterization of human APIP as an MtnB enzyme with a Km of 9.32 μM and a Vmax of 1.39 μmol min(-1) mg(-1)
GO:0051289 protein homotetramerization	IDA PMID:24367089 Structural and biochemical basis for the inhibition of cell ...	ACCEPT	Summary: Crystal structure and solution studies demonstrate APIP forms a homotetramer with C4 symmetry. "APIP/MtnB exists as a tetramer in solution and exhibits an assembly with C4 symmetry in the crystal lattice" (PMID:24367089). Reason: Structural evidence directly demonstrates tetrameric assembly, which is required for enzymatic function (active site is at subunit interface). Supporting Evidence: PMID:24367089 APIP/MtnB exists as a tetramer in solution and exhibits an assembly with C4 symmetry in the crystal lattice. The pocket-shaped active site is located at the end of a long cleft between two adjacent subunits.
GO:0070269 pyroptotic inflammatory response	IMP PMID:24367089 Structural and biochemical basis for the inhibition of cell ...	KEEP AS NON CORE	Summary: APIP inhibits caspase-1-dependent pyroptosis. Unlike its anti-apoptotic function, the anti-pyroptotic activity IS dependent on enzymatic activity. Kang et al. showed that enzymatic mutants lose the ability to protect against pyroptosis but retain anti-apoptotic activity (PMID:24367089). Reason: This represents a secondary regulatory function linked to the methionine salvage pathway. The inhibition of pyroptosis requires APIP's enzymatic activity, suggesting metabolic regulation of inflammation. However, this is not the primary function of APIP. Supporting Evidence: PMID:24367089 APIP/MtnB functions as a cell death inhibitor independently of its MtnB enzyme activity for apoptosis induced by either hypoxia or etoposide, but dependently for caspase-1-induced pyroptosis
GO:0005829 cytosol	TAS Reactome:R-HSA-6804596	ACCEPT	Summary: Reactome pathway annotation for APIP binding to the apoptosome complex (APAF1:CYCS). Cytosolic localization is consistent with immunofluorescence data (PMID:23285211). Reason: Cytosolic localization is consistent with experimental evidence and with APIP's role in both cytosolic methionine salvage and apoptosome regulation. Supporting Evidence: PMID:23285211 APIP was detected mainly in the cytoplasm of HeLa cells by immunofluorescence
GO:0019509 L-methionine salvage from methylthioadenosine	IMP PMID:22837397 Functional genetic screen of human diversity reveals that a ...	ACCEPT	Summary: Ko et al. (2012) confirmed APIP's role in methionine salvage through growth assays and MTA quantitation. "The role of APIP in methionine salvage was confirmed by growth assays with methionine-deficient media and quantitation of the methionine salvage substrate, 5'-methylthioadenosine" (PMID:22837397). Reason: This is the core biological process of APIP, demonstrated by functional mutant phenotype studies. Supporting Evidence: PMID:22837397 The role of APIP in methionine salvage was confirmed by growth assays with methionine-deficient media and quantitation of the methionine salvage substrate, 5'-methylthioadenosine
GO:0019509 L-methionine salvage from methylthioadenosine	IMP PMID:23285211 Functional identification of APIP as human mtnB, a key enzym...	ACCEPT	Summary: Mary et al. (2012) demonstrated that APIP knockdown impairs cell growth when methionine is replaced by MTA. "Stable knockdown of APIP specifically affects growth in MTA and depletes intracellular levels of methionine" (PMID:23285211). Reason: Independent IMP evidence confirming APIP's essential role in methionine salvage pathway. Supporting Evidence: PMID:23285211 We show that APIP depletion specifically impaired the capacity of cells to grow
GO:0043066 negative regulation of apoptotic process	IMP PMID:22837397 Functional genetic screen of human diversity reveals that a ...	KEEP AS NON CORE	Summary: Ko et al. showed that reduced APIP expression increases sensitivity to caspase-9-dependent cell death. "Consistent with APIP originally being identified as an inhibitor of caspase-9-dependent apoptosis, the same allele was also associated with increased sensitivity to the chemotherapeutic agent carboplatin" (PMID:22837397). Reason: This is a moonlighting function independent of enzymatic activity. It is a legitimate regulatory role but not the primary evolved function of APIP. Supporting Evidence: PMID:22837397 Consistent with APIP originally being identified as an inhibitor of caspase-9-dependent apoptosis, the same allele was also associated with increased sensitivity to the chemotherapeutic agent carboplatin
GO:0070372 regulation of ERK1 and ERK2 cascade	ISS GO_REF:0000024	UNDECIDED	Summary: Annotation transferred from mouse ortholog Q9WVQ5 by sequence similarity. Reason: Cannot evaluate without access to the primary evidence for the mouse annotation. This may represent a peripheral or context-dependent effect.

Core Functions

APIP is a zinc-dependent enzyme that catalyzes the dehydration of 5-methylthioribulose-1-phosphate (MTRu-1-P) to 2,3-diketo-5-methylthiopentyl-1-phosphate in the methionine salvage pathway. This is the primary evolved function of APIP, supported by structural data (PDB 4M6R), enzyme kinetics (Km = 9.32 uM), and functional studies demonstrating that APIP knockdown impairs methionine recycling from MTA.

Molecular Function:

methylthioribulose 1-phosphate dehydratase activity

Directly Involved In:

L-methionine salvage from methylthioadenosine

Cellular Locations:

cytosol

Supporting Evidence:

PMID:24367089
Here we report the structural and enzymatic characterization of human APIP as an MtnB enzyme with a Km of 9.32 μM and a Vmax of 1.39 μmol min(-1) mg(-1)
PMID:23285211
these results confirm the involvement of APIP in the methionine salvage pathway

References

GO_REF:0000024

Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000043

Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping

GO_REF:0000104

Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features

GO_REF:0000107

Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:16189514

Towards a proteome-scale map of the human protein-protein interaction network.

PMID:19060904

An empirical framework for binary interactome mapping.

PMID:22837397

Functional genetic screen of human diversity reveals that a methionine salvage enzyme regulates inflammatory cell death.

APIP role in methionine salvage confirmed

"The role of APIP in methionine salvage was confirmed by growth assays with methionine-deficient media and quantitation of the methionine salvage substrate, 5'-methylthioadenosine"
APIP variants affect susceptibility to both pyroptosis and apoptosis

"Reducing expression of APIP or exogenous addition of 5'-methylthioadenosine increased Salmonellae-induced cell death"
APIP inhibits caspase-1 and caspase-9 mediated cell death

"Consistent with APIP originally being identified as an inhibitor of caspase-9-dependent apoptosis, the same allele was also associated with increased sensitivity to the chemotherapeutic agent carboplatin"

PMID:23285211

Functional identification of APIP as human mtnB, a key enzyme in the methionine salvage pathway.

APIP is the human MtnB enzyme

"Using a bioinformatics approach, we propose that a protein called APIP could perform this role"
APIP knockdown impairs growth in MTA medium

"We show that APIP depletion specifically impaired the capacity of cells to grow"
APIP localizes to cytoplasm

"APIP was detected mainly in the cytoplasm of HeLa cells by immunofluorescence"
Two isoforms exist (long and short)

"Two splice isoforms are described for APIP (APIP.long and APIP.short)"

PMID:24367089

Structural and biochemical basis for the inhibition of cell death by APIP, a methionine salvage enzyme.

Crystal structure at 2.0 A (PDB 4M6R)

"The crystal structure was determined at 2.0-Å resolution, revealing an overall fold similar to members of the zinc-dependent class II aldolase family"
Km = 9.32 uM, Vmax = 1.39 umol/min/mg for MtnB reaction

"Here we report the structural and enzymatic characterization of human APIP as an MtnB enzyme with a Km of 9.32 μM and a Vmax of 1.39 μmol min(-1) mg(-1)"
Homotetramer with C4 symmetry

"APIP/MtnB exists as a tetramer in solution and exhibits an assembly with C4 symmetry in the crystal lattice"
Glu139 is catalytic acid/base

"We propose an enzymatic reaction mechanism involving Glu139* as a catalytic acid/base"
Anti-apoptotic activity is enzyme-independent

"APIP/MtnB functions as a cell death inhibitor independently of its MtnB enzyme activity for apoptosis induced by either hypoxia or etoposide"
Anti-pyroptotic activity is enzyme-dependent

"APIP/MtnB functions as a cell death inhibitor independently of its MtnB enzyme activity for apoptosis induced by either hypoxia or etoposide, but dependently for caspase-1-induced pyroptosis"

PMID:25416956

A proteome-scale map of the human interactome network.

PMID:27107014

An inter-species protein-protein interaction network across vast evolutionary distance.

PMID:29892012

An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders.

PMID:31515488

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.

PMID:32296183

A reference map of the human binary protein interactome.

PMID:32814053

Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.

PMID:33961781

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.

Reactome:R-HSA-6804596

APAF1:CYCS binds APIP

file:human/APIP/APIP-deep-research-falcon.md

Deep research report on APIP

APIP competes with procaspase-9 for Apaf-1 binding

"APIP competes with procaspase-9 for Apaf-1 binding, inhibiting apoptosome-driven caspase-9 activation and offering cytoprotection in hypoxia/ischemia models"
Enzymatic activity dispensable for anti-apoptotic effects

"APIP's enzymatic activity is dispensable for anti-apoptotic effects under hypoxia/etoposide, but required for suppression of caspase-1-dependent pyroptosis"

📚 Additional Documentation

Deep Research Falcon

(APIP-deep-research-falcon.md)

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organism: human
gene_id: APIP
gene_symbol: APIP
uniprot_accession: Q96GX9
protein_description: 'RecName: Full=Methylthioribulose-1-phosphate dehydratase {ECO:0000255|HAMAP-Rule:MF_03116};
Short=MTRu-1-P dehydratase {ECO:0000255|HAMAP-Rule:MF_03116}; EC=4.2.1.109 {ECO:0000255|HAMAP-Rule:MF_03116,
ECO:0000269|PubMed:24367089}; AltName: Full=APAF1-interacting protein {ECO:0000255|HAMAP-Rule:MF_03116};
Short=hAPIP;'
gene_info: Name=APIP {ECO:0000255|HAMAP-Rule:MF_03116}; ORFNames=CGI-29;
organism_full: Homo sapiens (Human).
protein_family: Belongs to the aldolase class II family. MtnB subfamily.
protein_domains: Aldolase_II/adducin_N. (IPR001303); Aldolase_II/adducin_N_sf. (IPR036409);
MethylthioRu-1-P_deHdtase_MtnB. (IPR017714); Salvage_MtnB_euk. (IPR027514); Aldolase_II
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Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

UniProt Accession: Q96GX9
Protein Description: RecName: Full=Methylthioribulose-1-phosphate dehydratase {ECO:0000255|HAMAP-Rule:MF_03116}; Short=MTRu-1-P dehydratase {ECO:0000255|HAMAP-Rule:MF_03116}; EC=4.2.1.109 {ECO:0000255|HAMAP-Rule:MF_03116, ECO:0000269|PubMed:24367089}; AltName: Full=APAF1-interacting protein {ECO:0000255|HAMAP-Rule:MF_03116}; Short=hAPIP;
Gene Information: Name=APIP {ECO:0000255|HAMAP-Rule:MF_03116}; ORFNames=CGI-29;
Organism (full): Homo sapiens (Human).
Protein Family: Belongs to the aldolase class II family. MtnB subfamily.
Key Domains: Aldolase_II/adducin_N. (IPR001303); Aldolase_II/adducin_N_sf. (IPR036409); MethylthioRu-1-P_deHdtase_MtnB. (IPR017714); Salvage_MtnB_euk. (IPR027514); Aldolase_II (PF00596)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "APIP" matches the protein description above
Verify the organism is correct: Homo sapiens (Human).
Check if protein family/domains align with what you find in literature
If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'APIP' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene APIP (gene ID: APIP, UniProt: Q96GX9) in human.

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Output

Question: You are an expert researcher providing comprehensive, well-cited information.

Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies

Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

UniProt Accession: Q96GX9
Protein Description: RecName: Full=Methylthioribulose-1-phosphate dehydratase {ECO:0000255|HAMAP-Rule:MF_03116}; Short=MTRu-1-P dehydratase {ECO:0000255|HAMAP-Rule:MF_03116}; EC=4.2.1.109 {ECO:0000255|HAMAP-Rule:MF_03116, ECO:0000269|PubMed:24367089}; AltName: Full=APAF1-interacting protein {ECO:0000255|HAMAP-Rule:MF_03116}; Short=hAPIP;
Gene Information: Name=APIP {ECO:0000255|HAMAP-Rule:MF_03116}; ORFNames=CGI-29;
Organism (full): Homo sapiens (Human).
Protein Family: Belongs to the aldolase class II family. MtnB subfamily.
Key Domains: Aldolase_II/adducin_N. (IPR001303); Aldolase_II/adducin_N_sf. (IPR036409); MethylthioRu-1-P_deHdtase_MtnB. (IPR017714); Salvage_MtnB_euk. (IPR027514); Aldolase_II (PF00596)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "APIP" matches the protein description above
Verify the organism is correct: Homo sapiens (Human).
Check if protein family/domains align with what you find in literature
If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

Research Target:

Please provide a comprehensive research report on the gene APIP (gene ID: APIP, UniProt: Q96GX9) in human.

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Research plan status: All objectives completed. We verified identity, gathered foundational and recent literature, extracted quantitative data, and created a concise evidence table.

Gene/protein identity verification
APIP (UniProt Q96GX9) encodes the human 5-methylthioribulose-1-phosphate dehydratase (MtnB; EC 4.2.1.109), historically identified as “Apaf-1–interacting protein.” Foundational and structural studies conclusively assign APIP to the eukaryotic MtnB subfamily of aldolase class II enzymes with a zinc-dependent active site, in Homo sapiens. No conflicting gene symbol usage was identified within the retrieved evidence (camille2012functionalidentificationof pages 1-3, kang2014structuralandbiochemical pages 1-2).

Key concepts and definitions with current understanding
- Primary biochemical function and reaction: APIP catalyzes the dehydration of 5-methylthioribulose-1-phosphate (MTRu-1-P) to the 2,3-diketo intermediate (commonly detected via formation of 2-keto-4-methylthiobutyrate equivalents through coupled assays), constituting the MtnB step of the methionine salvage (MTA) pathway that recycles 5′-methylthioadenosine sulfur to methionine (EC 4.2.1.109). Knockdown of APIP impairs growth when methionine is replaced by MTA and lowers cellular methionine, demonstrating requirement for methionine recycling from MTA in human cells (URL: https://doi.org/10.1371/journal.pone.0052877; published 28 Dec 2012) (camille2012functionalidentificationof pages 5-5, camille2012functionalidentificationof pages 1-3, camille2012functionalidentificationof pages 3-4).
- Structural class and domains: APIP adopts a class II aldolase-like fold and assembles as a tetramer. A 2.0-Å crystal structure (PDB 4M6R) reveals an active-site zinc coordinated by histidines and substrate oxygens; Glu139 functions as a catalytic acid/base, with additional important residues Cys97 and His115. Kinetic parameters measured in vitro are Km ≈ 9.32 μM and Vmax ≈ 1.39 μmol·min−1·mg−1 for the MtnB reaction (URL: https://doi.org/10.1073/pnas.1308768111; online 23 Dec 2013; print 2014) (kang2014structuralandbiochemical pages 1-2, kang2014structuralandbiochemical pages 8-8, kang2014structuralandbiochemical pages 2-3, kang2014structuralandbiochemical pages 4-6).
- Cellular localization and isoforms: Immunofluorescence showed predominant cytosolic staining in HeLa cells. Two APIP transcript isoforms (long 729 bp and short 628 bp) were cloned; the short isoform lacks N-terminal residues required for enzymatic activity (URL: https://doi.org/10.1371/journal.pone.0052877; 28 Dec 2012) (camille2012functionalidentificationof pages 1-3).

Recent developments and latest research (prioritize 2023–2024)
- Apoptosome regulation context: A 2024 expert review synthesizes regulators of apoptotic decision making, including modulators of Apaf-1 and apoptosome activity, and situates APIP among Apaf-1–interacting proteins of relevance in oncology. While not an APIP-specific primary study, it provides updated expert analysis connecting apoptosome modulation to disease (URL: https://doi.org/10.3390/biom14010136; Jan 2024) (kang2014structuralandbiochemical pages 8-8).
- Note on scarcity of 2023–2024 APIP-specific primary data: Within the retrieved evidence, no new peer-reviewed primary articles from 2023–2024 directly revising APIP’s enzymology or human functional assignment were identified. The field continues to reference the 2012–2014 primary studies for APIP’s enzymatic identity and structure (kang2014structuralandbiochemical pages 8-8, kang2014structuralandbiochemical pages 1-2).

Current applications and real-world implementations
- Pathway and metabolic context: APIP’s MtnB step is essential for efficient methionine salvage from MTA, relevant to cell proliferation in methionine-limited or MTA-rich contexts and to host–pathogen interactions where host methionine availability constrains intracellular bacterial growth (Shigella methionine auxotroph proliferation is impeded in APIP-knockdown host cells) (URL: https://doi.org/10.1371/journal.pone.0052877; 28 Dec 2012) (camille2012functionalidentificationof pages 5-5, camille2012functionalidentificationof pages 1-3).
- Cell-death modulation: APIP competes with procaspase-9 for Apaf-1 binding, inhibiting apoptosome-driven caspase-9 activation and offering cytoprotection in hypoxia/ischemia models; APIP’s enzymatic activity is dispensable for anti-apoptotic effects under hypoxia/etoposide, but required for suppression of caspase‑1–dependent pyroptosis, linking sulfur metabolic flux to inflammasome outputs (URL: https://doi.org/10.1073/pnas.1308768111; 23 Dec 2013/2014; URL: https://doi.org/10.1074/jbc.m405747200; Sep 2004) (kang2014structuralandbiochemical pages 4-6, cho2004inducedinhibitionof pages 1-1).

Expert opinions and analysis from authoritative sources
- Structural biochemistry and apoptosis/pyroptosis linkage: Kang et al. provide authoritative structural and mechanistic analysis demonstrating the active-site organization, mutational effects (Q96A ~36% activity; C97A/E139A/H115A <6%), and the differential requirement of enzymatic activity for pyroptosis vs apoptosis inhibition—an observation shaping how APIP is interpreted as both a metabolic enzyme and a signaling modulator (URL: https://doi.org/10.1073/pnas.1308768111; 2013/2014) (kang2014structuralandbiochemical pages 4-6, kang2014structuralandbiochemical pages 2-3).
- Apoptosome modulation landscape (2024 review): The Biomolecules review integrates Apaf‑1 regulators, with APIP included among proteins that can influence apoptosome assembly/activity, underscoring disease relevance in cancer and therapy resistance contexts (URL: https://doi.org/10.3390/biom14010136; Jan 2024) (kang2014structuralandbiochemical pages 8-8).

Relevant statistics and data from recent studies
- Enzyme kinetics: Km ≈ 9.32 μM; Vmax ≈ 1.39 μmol·min−1·mg−1 for the MTRu‑1‑P dehydratase reaction; tetrameric assembly validated by crystallography and solution studies (URL: https://doi.org/10.1073/pnas.1308768111; 2013/2014) (kang2014structuralandbiochemical pages 1-2, kang2014structuralandbiochemical pages 2-3).
- Mutational impacts on catalysis: Q96A retains ~36.2% activity; C97A, E139A, H115A each <6% residual activity, supporting roles in substrate positioning and acid/base catalysis (URL: https://doi.org/10.1073/pnas.1308768111; 2013/2014) (kang2014structuralandbiochemical pages 4-6).
- Localization and isoform dependence: Cytosolic localization; short N-terminally truncated isoform inactive in assays, indicating N-terminus importance for function (URL: https://doi.org/10.1371/journal.pone.0052877; 28 Dec 2012) (camille2012functionalidentificationof pages 1-3).
- Disease associations (expression): Down-regulation of APIP reported in non-small cell lung carcinoma tissue cohorts (URL: https://doi.org/10.3892/ijo.2012.1397; Mar 2012) (kang2014structuralandbiochemical pages 2-3). Additional tumor types with altered APIP expression are noted in structural/biochemical context discussions (e.g., squamous carcinomas), though cohort-level quantitation resides in cited datasets within those studies (URL: https://doi.org/10.1073/pnas.1308768111; 2013/2014) (kang2014structuralandbiochemical pages 2-3).

Mechanistic summary of signaling and biochemical pathways
- Methionine salvage pathway (MTA cycle): APIP (MtnB) converts MTRu‑1‑P to the 2,3‑diketo‑5‑methylthiopentyl‑1‑phosphate intermediate, enabling subsequent steps that regenerate methionine from MTA. Loss of APIP curtails methionine recycling and cell growth under methionine replacement by MTA (URL: https://doi.org/10.1371/journal.pone.0052877; 2012) (camille2012functionalidentificationof pages 5-5, camille2012functionalidentificationof pages 1-3, camille2012functionalidentificationof pages 3-4).
- Apoptosome/caspase pathway: APIP binds Apaf‑1 and competes with procaspase‑9 to attenuate apoptosome activation, protecting cells from mitochondrial pathway apoptosis under hypoxia/ischemia and genotoxic stress; in parallel, APIP’s enzymatic role modulates caspase‑1–dependent pyroptosis, making APIP a dual-function node at the metabolism–cell death interface (URLs: https://doi.org/10.1074/jbc.m405747200; 2004 and https://doi.org/10.1073/pnas.1308768111; 2013/2014) (cho2004inducedinhibitionof pages 1-1, kang2014structuralandbiochemical pages 4-6).

Limitations and open questions
- 2023–2024 primary updates on APIP’s human enzymology, structure, or new interactors are limited within available evidence. The 2024 review supports continuing relevance of apoptosome modulators but does not overturn earlier APIP findings. Further population-level genomics and disease association studies focused specifically on APIP remain needed (kang2014structuralandbiochemical pages 8-8).

Embedded evidence table
| Year | Citation (first author et al.) | Key finding (1-2 sentences) | Topic tags | Journal | DOI / URL | Publication date |
|------|-------------------------------|-----------------------------|------------|---------|-----------|------------------|
| 2012 | Mary et al. | Functionally identified APIP as human MtnB (methylthioribulose-1-phosphate dehydratase) required for methionine salvage; cytosolic localization, two isoforms, and a zinc-binding site required for activity (camille2012functionalidentificationof pages 1-3). | enzymology, localization, isoforms, metal-dependence | PLoS ONE | https://doi.org/10.1371/journal.pone.0052877 | 28 Dec 2012 (published) |
| 2014 | Kang et al. | 2.0 Å crystal structure (PDB 4M6R) confirms class II aldolase fold with active-site Zn; kinetics Km = 9.32 µM, Vmax = 1.39 µmol·min⁻¹·mg⁻¹; APIP inhibits caspase-9-dependent apoptosis (Apaf-1 competition) and Zn-dependent enzymatic activity is required to inhibit caspase-1 pyroptosis (kang2014structuralandbiochemical pages 4-6). | structure, enzymology, apoptosis, pyroptosis | Proceedings of the National Academy of Sciences (PNAS) | https://doi.org/10.1073/pnas.1308768111 | 23 Dec 2013 (online); 2014 (print) |
| 2004 | Cho et al. | Identified APIP as an Apaf-1–interacting protein that binds the Apaf-1 CARD and competes with procaspase-9, protecting skeletal muscle cells from ischemia/hypoxia-induced apoptosis (cho2004inducedinhibitionof pages 1-2). | apoptosis, protein–protein interaction, ischemia | Journal of Biological Chemistry (JBC) | https://doi.org/10.1074/jbc.m405747200 | Sep 2004 |
| 2012 | Moravcikova et al. | Reported down-regulated expression of apoptosis-associated gene APIP in non-small cell lung carcinoma, supporting tumor-associated expression changes of APIP (reported in oncology datasets; see supporting structural/expression summaries) (kang2014structuralandbiochemical pages 2-3). | expression, cancer association (NSCLC) | International Journal of Oncology | https://doi.org/10.3892/ijo.2012.1397 | Mar 2012 |
| 2024 | Abbas et al. | Recent review on apoptosis regulators summarizes Apaf-1 regulatory network and places APIP/APAF1 interactions in broader context of apoptosome modulation and cancer relevance (kang2014structuralandbiochemical pages 8-8). | review, apoptosis regulation, expert analysis | Biomolecules | https://doi.org/10.3390/biom14010136 | Jan 2024 |

Table: Concise summary table of foundational and recent sources for human APIP (Q96GX9), showing main findings, topics, journals, and DOIs to support functional annotation and literature citations.

Conclusion
Human APIP (Q96GX9) is a zinc-dependent class II aldolase family enzyme that executes the MtnB step of the methionine salvage pathway and, through interaction with Apaf‑1, modulates apoptosome activity and apoptosis. Structural, biochemical, and cellular evidence converge to define its catalytic mechanism, cellular localization, and dual roles in apoptosis and pyroptosis. Recent expert reviews (2024) reaffirm the importance of apoptosome regulators, including APIP, in disease, while primary APIP-specific advances since 2014 were not identified within the retrieved sources (camille2012functionalidentificationof pages 1-3, kang2014structuralandbiochemical pages 1-2, kang2014structuralandbiochemical pages 4-6, cho2004inducedinhibitionof pages 1-1, kang2014structuralandbiochemical pages 2-3, kang2014structuralandbiochemical pages 8-8).

References

(camille2012functionalidentificationof pages 1-3): Camille Mary, Paula Duek, Lisa Salleron, Petra Tienz, Dirk Bumann, Amos Bairoch, and Lydie Lane. Functional identification of apip as human mtnb, a key enzyme in the methionine salvage pathway. PLoS ONE, 7:e52877, Dec 2012. URL: https://doi.org/10.1371/journal.pone.0052877, doi:10.1371/journal.pone.0052877. This article has 27 citations and is from a peer-reviewed journal.
(kang2014structuralandbiochemical pages 1-2): Wonchull Kang, Se Hoon Hong, Hye Min Lee, Na Yeon Kim, Yun Chan Lim, Le Thi My Le, Bitna Lim, Hyun Chul Kim, Tae Yeon Kim, Hiroki Ashida, Akiho Yokota, Sang Soo Hah, Keun Ho Chun, Yong-Keun Jung, and Jin Kuk Yang. Structural and biochemical basis for the inhibition of cell death by apip, a methionine salvage enzyme. Proceedings of the National Academy of Sciences, 111:E54-E61, Dec 2014. URL: https://doi.org/10.1073/pnas.1308768111, doi:10.1073/pnas.1308768111. This article has 39 citations and is from a highest quality peer-reviewed journal.
(camille2012functionalidentificationof pages 5-5): Camille Mary, Paula Duek, Lisa Salleron, Petra Tienz, Dirk Bumann, Amos Bairoch, and Lydie Lane. Functional identification of apip as human mtnb, a key enzyme in the methionine salvage pathway. PLoS ONE, 7:e52877, Dec 2012. URL: https://doi.org/10.1371/journal.pone.0052877, doi:10.1371/journal.pone.0052877. This article has 27 citations and is from a peer-reviewed journal.
(camille2012functionalidentificationof pages 3-4): Camille Mary, Paula Duek, Lisa Salleron, Petra Tienz, Dirk Bumann, Amos Bairoch, and Lydie Lane. Functional identification of apip as human mtnb, a key enzyme in the methionine salvage pathway. PLoS ONE, 7:e52877, Dec 2012. URL: https://doi.org/10.1371/journal.pone.0052877, doi:10.1371/journal.pone.0052877. This article has 27 citations and is from a peer-reviewed journal.
(kang2014structuralandbiochemical pages 8-8): Wonchull Kang, Se Hoon Hong, Hye Min Lee, Na Yeon Kim, Yun Chan Lim, Le Thi My Le, Bitna Lim, Hyun Chul Kim, Tae Yeon Kim, Hiroki Ashida, Akiho Yokota, Sang Soo Hah, Keun Ho Chun, Yong-Keun Jung, and Jin Kuk Yang. Structural and biochemical basis for the inhibition of cell death by apip, a methionine salvage enzyme. Proceedings of the National Academy of Sciences, 111:E54-E61, Dec 2014. URL: https://doi.org/10.1073/pnas.1308768111, doi:10.1073/pnas.1308768111. This article has 39 citations and is from a highest quality peer-reviewed journal.
(kang2014structuralandbiochemical pages 2-3): Wonchull Kang, Se Hoon Hong, Hye Min Lee, Na Yeon Kim, Yun Chan Lim, Le Thi My Le, Bitna Lim, Hyun Chul Kim, Tae Yeon Kim, Hiroki Ashida, Akiho Yokota, Sang Soo Hah, Keun Ho Chun, Yong-Keun Jung, and Jin Kuk Yang. Structural and biochemical basis for the inhibition of cell death by apip, a methionine salvage enzyme. Proceedings of the National Academy of Sciences, 111:E54-E61, Dec 2014. URL: https://doi.org/10.1073/pnas.1308768111, doi:10.1073/pnas.1308768111. This article has 39 citations and is from a highest quality peer-reviewed journal.
(kang2014structuralandbiochemical pages 4-6): Wonchull Kang, Se Hoon Hong, Hye Min Lee, Na Yeon Kim, Yun Chan Lim, Le Thi My Le, Bitna Lim, Hyun Chul Kim, Tae Yeon Kim, Hiroki Ashida, Akiho Yokota, Sang Soo Hah, Keun Ho Chun, Yong-Keun Jung, and Jin Kuk Yang. Structural and biochemical basis for the inhibition of cell death by apip, a methionine salvage enzyme. Proceedings of the National Academy of Sciences, 111:E54-E61, Dec 2014. URL: https://doi.org/10.1073/pnas.1308768111, doi:10.1073/pnas.1308768111. This article has 39 citations and is from a highest quality peer-reviewed journal.
(cho2004inducedinhibitionof pages 1-1): Dong-Hyung Cho, Yeon-Mi Hong, Ho-June Lee, Ha-Na Woo, Jong-Ok Pyo, Tak W. Mak, and Yong-Keun Jung. Induced inhibition of ischemic/hypoxic injury by apip, a novel apaf-1-interacting protein*. Journal of Biological Chemistry, 279:39942-39950, Sep 2004. URL: https://doi.org/10.1074/jbc.m405747200, doi:10.1074/jbc.m405747200. This article has 93 citations and is from a domain leading peer-reviewed journal.
(cho2004inducedinhibitionof pages 1-2): Dong-Hyung Cho, Yeon-Mi Hong, Ho-June Lee, Ha-Na Woo, Jong-Ok Pyo, Tak W. Mak, and Yong-Keun Jung. Induced inhibition of ischemic/hypoxic injury by apip, a novel apaf-1-interacting protein*. Journal of Biological Chemistry, 279:39942-39950, Sep 2004. URL: https://doi.org/10.1074/jbc.m405747200, doi:10.1074/jbc.m405747200. This article has 93 citations and is from a domain leading peer-reviewed journal.

Citations

camille2012functionalidentificationof pages 1-3
kang2014structuralandbiochemical pages 8-8
kang2014structuralandbiochemical pages 4-6
kang2014structuralandbiochemical pages 2-3
cho2004inducedinhibitionof pages 1-2
kang2014structuralandbiochemical pages 1-2
camille2012functionalidentificationof pages 5-5
camille2012functionalidentificationof pages 3-4
cho2004inducedinhibitionof pages 1-1
https://doi.org/10.1371/journal.pone.0052877;
https://doi.org/10.1073/pnas.1308768111;
https://doi.org/10.3390/biom14010136;
https://doi.org/10.1074/jbc.m405747200;
https://doi.org/10.3892/ijo.2012.1397;
https://doi.org/10.1371/journal.pone.0052877
https://doi.org/10.1073/pnas.1308768111
https://doi.org/10.1074/jbc.m405747200
https://doi.org/10.3892/ijo.2012.1397
https://doi.org/10.3390/biom14010136
https://doi.org/10.1371/journal.pone.0052877,
https://doi.org/10.1073/pnas.1308768111,
https://doi.org/10.1074/jbc.m405747200,

📄 View Raw YAML

id: Q96GX9
gene_symbol: APIP
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  APIP (also known as MtnB) is a zinc-dependent methylthioribulose-1-phosphate dehydratase
  that catalyzes the dehydration of MTRu-1-P to 2,3-diketo-5-methylthiopentyl-1-phosphate
  in the methionine salvage pathway. This is its primary evolved enzymatic function.
  The
  protein also has a moonlighting function as an inhibitor of apoptosis through competitive
  binding to Apaf-1, which is independent of its enzymatic activity. Additionally,
  APIP
  inhibits caspase-1-dependent pyroptosis in an enzyme-activity-dependent manner.
  The
  protein exists as a homotetramer and is localized in the cytoplasm.
existing_annotations:
  - term:
      id: GO:0005737
      label: cytoplasm
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        APIP is localized to the cytoplasm. Immunofluorescence studies showed "APIP
        was
        detected mainly in the cytoplasm of HeLa cells" (PMID:23285211). The IBA annotation
        from phylogenetic inference is consistent with experimental evidence.
      action: ACCEPT
      reason: >-
        Cytoplasmic localization is well-supported by immunofluorescence data (PMID:23285211)
        and is consistent with its role in the cytosolic methionine salvage pathway.
      supported_by:
        - reference_id: PMID:23285211
          supporting_text: "In accordance with its putative role in the methionine
            salvage pathway, APIP was detected mainly in the cytoplasm of HeLa cells
            by immunofluorescence"
  - term:
      id: GO:0019509
      label: L-methionine salvage from methylthioadenosine
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        APIP functions as MtnB in the methionine salvage pathway. This is its primary
        enzymatic function. Knockdown studies showed that "APIP depletion specifically
        impaired the capacity of cells to grow" when methionine was replaced by MTA
        (PMID:23285211). Ko et al. (2012) confirmed "The role of APIP in methionine
        salvage
        was confirmed by growth assays with methionine-deficient media and quantitation
        of
        the methionine salvage substrate, 5'-methylthioadenosine" (PMID:22837397).
      action: ACCEPT
      reason: >-
        This represents the core evolved function of APIP. Multiple studies demonstrate
        APIP's essential role in the methionine salvage pathway through functional
        assays.
      supported_by:
        - reference_id: PMID:23285211
          supporting_text: "We show that APIP depletion specifically impaired the
            capacity of cells to grow"
        - reference_id: PMID:22837397
          supporting_text: "The role of APIP in methionine salvage was confirmed by
            growth assays with methionine-deficient media and quantitation of the
            methionine salvage substrate, 5'-methylthioadenosine"
  - term:
      id: GO:0046570
      label: methylthioribulose 1-phosphate dehydratase activity
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        APIP catalyzes the dehydration of MTRu-1-P with measured kinetic parameters
        of
        Km ~9.32 uM and Vmax ~1.39 umol/min/mg (PMID:24367089). The crystal structure
        at 2.0 A resolution (PDB 4M6R) confirms a class II aldolase fold with active-site
        zinc. This is the core molecular function of APIP.
      action: ACCEPT
      reason: >-
        This is the primary molecular function of APIP, well-characterized structurally
        and biochemically.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "Here we report the structural and enzymatic characterization
            of human APIP as an MtnB enzyme with a Km of 9.32 μM and a Vmax of 1.39
            μmol min(-1) mg(-1)"
  - term:
      id: GO:0005737
      label: cytoplasm
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: >-
        IEA annotation for cytoplasm based on InterPro domains and UniProt subcellular
        location data. Consistent with experimental IDA evidence from PMID:23285211.
      action: ACCEPT
      reason: >-
        Consistent with experimental evidence; duplicates IBA and IDA annotations
        but
        this is acceptable as it represents an independent computational prediction
        that agrees with experimental data.
      supported_by:
        - reference_id: PMID:23285211
          supporting_text: "APIP was detected mainly in the cytoplasm of HeLa cells
            by immunofluorescence"
  - term:
      id: GO:0006915
      label: apoptotic process
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >-
        This annotation is an OVER-ANNOTATION. APIP does not participate in apoptosis
        -
        it INHIBITS apoptosis as a moonlighting function separate from its enzymatic
        activity. Kang et al. (2014) demonstrated that "APIP/MtnB functions as a cell
        death inhibitor independently of its MtnB enzyme activity for apoptosis induced
        by either hypoxia or etoposide" (PMID:24367089). The gene was named "APAF1-interacting
        protein" because it binds Apaf-1 CARD and competes with procaspase-9, thereby
        inhibiting apoptosome formation. GO:0006915 (apoptotic process) implies direct
        participation in apoptosis, which is inappropriate for an inhibitor.
      action: MARK_AS_OVER_ANNOTATED
      reason: >-
        APIP is an INHIBITOR of apoptosis, not a participant. The IEA mapping from
        UniProt
        keyword "Apoptosis" does not distinguish between proteins that participate
        in
        apoptosis and those that regulate/inhibit it. The proper annotation would
        be
        GO:0043066 (negative regulation of apoptotic process), which is already annotated
        with IMP evidence.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "APIP/MtnB functions as a cell death inhibitor independently
            of its MtnB enzyme activity for apoptosis induced by either hypoxia or
            etoposide"
        - reference_id: PMID:24367089
          supporting_text: "APIP, Apaf-1 interacting protein, has been known to inhibit
            two main types of programmed cell death, apoptosis and pyroptosis"
        - reference_id: file:human/APIP/APIP-deep-research-falcon.md
          supporting_text: "APIP competes with procaspase-9 for Apaf-1 binding, inhibiting
            apoptosome-driven caspase-9 activation and offering cytoprotection in
            hypoxia/ischemia models"
  - term:
      id: GO:0008270
      label: zinc ion binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000104
    review:
      summary: >-
        APIP is a zinc-dependent enzyme. The crystal structure (PDB 4M6R) shows zinc
        coordination by His115, His117, and His195 (PMID:24367089). UniProt notes
        "Binds
        1 zinc ion per subunit." IEA is consistent with IDA evidence.
      action: ACCEPT
      reason: >-
        Zinc binding is essential for catalytic activity and is demonstrated in the
        crystal structure. The IEA annotation is consistent with experimental IDA
        evidence.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "an overall fold similar to members of the zinc-dependent
            class II aldolase family"
  - term:
      id: GO:0008652
      label: amino acid biosynthetic process
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >-
        The methionine salvage pathway regenerates methionine from 5'-methylthioadenosine.
        While technically methionine biosynthesis, GO:0019509 (L-methionine salvage
        from
        methylthioadenosine) is more specific and appropriate. This general term is
        acceptable but less informative.
      action: ACCEPT
      reason: >-
        APIP does participate in amino acid biosynthesis (methionine salvage), though
        the more specific term GO:0019509 is preferred and already annotated.
      supported_by:
        - reference_id: PMID:23285211
          supporting_text: "these results confirm the involvement of APIP in the methionine
            salvage pathway"
  - term:
      id: GO:0016829
      label: lyase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >-
        APIP has EC 4.2.1.109 (lyase activity). The more specific term GO:0046570
        (methylthioribulose 1-phosphate dehydratase activity) is already annotated
        with IDA evidence. This general lyase annotation is acceptable but less informative.
      action: ACCEPT
      reason: >-
        APIP is indeed a lyase (EC 4.2.1.109). The annotation is correct but the more
        specific GO:0046570 is preferred and already present.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "5-methylthioribulose-1-phosphate dehydratase, or MtnB,
            in the methionine salvage pathway"
  - term:
      id: GO:0019509
      label: L-methionine salvage from methylthioadenosine
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: >-
        IEA annotation for methionine salvage based on InterPro domains. Consistent
        with IBA and IMP evidence for this annotation.
      action: ACCEPT
      reason: >-
        This is the core biological process for APIP. The IEA annotation from domain
        analysis agrees with experimental evidence.
      supported_by:
        - reference_id: PMID:23285211
          supporting_text: "these results confirm the involvement of APIP in the methionine
            salvage pathway"
  - term:
      id: GO:0046570
      label: methylthioribulose 1-phosphate dehydratase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: >-
        IEA annotation for the dehydratase activity based on Rhea reaction mapping
        (EC:4.2.1.109). Consistent with IDA evidence from PMID:24367089.
      action: ACCEPT
      reason: >-
        This is the core molecular function of APIP. The computational annotation
        agrees with direct enzyme assay data.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "Here we report the structural and enzymatic characterization
            of human APIP as an MtnB enzyme with a Km of 9.32 μM and a Vmax of 1.39
            μmol min(-1) mg(-1)"
  - term:
      id: GO:0046872
      label: metal ion binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: >-
        APIP binds zinc as a cofactor. The more specific GO:0008270 (zinc ion binding)
        is already annotated. This general metal ion binding annotation is correct
        but
        less informative.
      action: ACCEPT
      reason: >-
        APIP binds zinc ions. The annotation is correct, though the more specific
        zinc ion binding term is preferred.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "zinc-dependent class II aldolase family"
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:16189514
    review:
      summary: >-
        High-throughput protein-protein interaction study. "Protein binding" is
        uninformative and should generally be avoided per curation guidelines.
      action: REMOVE
      reason: >-
        "Protein binding" does not tell us about the actual function of APIP. The
        interaction detected is likely part of high-throughput screening and does
        not represent a specific functional interaction. More informative terms like
        "identical protein binding" for homomeric interactions are preferred.
      supported_by:
        - reference_id: PMID:16189514
          supporting_text: Towards a proteome-scale map of the human 
            protein-protein interaction network.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:19060904
    review:
      summary: >-
        High-throughput interactome mapping study. Uninformative term.
      action: REMOVE
      reason: >-
        "Protein binding" is too vague and uninformative about APIP's actual function.
      supported_by:
        - reference_id: PMID:19060904
          supporting_text: An empirical framework for binary interactome 
            mapping.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:25416956
    review:
      summary: >-
        Proteome-scale interactome mapping. Generic protein binding annotation.
      action: REMOVE
      reason: >-
        "Protein binding" is uninformative. High-throughput interaction data should
        be represented by more specific binding terms where possible.
      supported_by:
        - reference_id: PMID:25416956
          supporting_text: A proteome-scale map of the human interactome 
            network.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:27107014
    review:
      summary: >-
        Inter-species protein-protein interaction study. Generic annotation.
      action: REMOVE
      reason: >-
        Uninformative term from high-throughput study.
      supported_by:
        - reference_id: PMID:27107014
          supporting_text: An inter-species protein-protein interaction network 
            across vast evolutionary distance.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:29892012
    review:
      summary: >-
        High-throughput interactome perturbation study. Generic annotation.
      action: REMOVE
      reason: >-
        Uninformative term.
      supported_by:
        - reference_id: PMID:29892012
          supporting_text: Jun 11. An interactome perturbation framework 
            prioritizes damaging missense mutations for developmental disorders.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:31515488
    review:
      summary: >-
        Study on genetic variants affecting protein interactions. Generic annotation.
      action: REMOVE
      reason: >-
        Uninformative term from high-throughput study.
      supported_by:
        - reference_id: PMID:31515488
          supporting_text: Extensive disruption of protein interactions by 
            genetic variants across the allele frequency spectrum in human 
            populations.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:32296183
    review:
      summary: >-
        Reference map of human binary interactome. Generic protein binding annotation.
      action: REMOVE
      reason: >-
        Uninformative. The identical protein binding annotation (GO:0042802) from
        the
        same reference is more informative.
      supported_by:
        - reference_id: PMID:32296183
          supporting_text: Apr 8. A reference map of the human binary protein 
            interactome.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:32814053
    review:
      summary: >-
        Interactome mapping for neurodegenerative disease proteins. Generic annotation.
      action: REMOVE
      reason: >-
        Uninformative term.
      supported_by:
        - reference_id: PMID:32814053
          supporting_text: Interactome Mapping Provides a Network of 
            Neurodegenerative Disease Proteins and Uncovers Widespread Protein 
            Aggregation in Affected Brains.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:33961781
    review:
      summary: >-
        Dual proteome-scale networks study. Generic protein binding annotation.
      action: REMOVE
      reason: >-
        Uninformative term from high-throughput study.
      supported_by:
        - reference_id: PMID:33961781
          supporting_text: 2021 May 6. Dual proteome-scale networks reveal 
            cell-specific remodeling of the human interactome.
  - term:
      id: GO:0042802
      label: identical protein binding
    evidence_type: IPI
    original_reference_id: PMID:16189514
    review:
      summary: >-
        APIP forms homotetramers. The crystal structure (PDB 4M6R) shows "APIP/MtnB
        exists as a tetramer in solution and exhibits an assembly with C4 symmetry"
        (PMID:24367089). Identical protein binding is appropriate for homooligomeric
        proteins.
      action: ACCEPT
      reason: >-
        APIP is a homotetramer, and self-interaction is required for its enzymatic
        function. The annotation accurately reflects the protein's quaternary structure.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "APIP/MtnB exists as a tetramer in solution and exhibits
            an assembly with C4 symmetry in the crystal lattice"
        - reference_id: PMID:16189514
          supporting_text: Towards a proteome-scale map of the human 
            protein-protein interaction network.
  - term:
      id: GO:0042802
      label: identical protein binding
    evidence_type: IPI
    original_reference_id: PMID:19060904
    review:
      summary: >-
        Duplicate annotation for APIP homotetrameric assembly. Same rationale as above.
      action: ACCEPT
      reason: >-
        Consistent with structural evidence for homotetramer formation.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "APIP/MtnB exists as a tetramer in solution"
        - reference_id: PMID:19060904
          supporting_text: An empirical framework for binary interactome 
            mapping.
  - term:
      id: GO:0042802
      label: identical protein binding
    evidence_type: IPI
    original_reference_id: PMID:25416956
    review:
      summary: >-
        Additional evidence for APIP self-interaction/homotetramer formation.
      action: ACCEPT
      reason: >-
        Consistent with structural and biochemical evidence.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "APIP/MtnB exists as a tetramer in solution"
        - reference_id: PMID:25416956
          supporting_text: A proteome-scale map of the human interactome 
            network.
  - term:
      id: GO:0042802
      label: identical protein binding
    evidence_type: IPI
    original_reference_id: PMID:31515488
    review:
      summary: >-
        APIP self-interaction detected in genetic variant study.
      action: ACCEPT
      reason: >-
        Consistent with known homotetrameric structure.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "APIP/MtnB exists as a tetramer in solution"
        - reference_id: PMID:31515488
          supporting_text: Extensive disruption of protein interactions by 
            genetic variants across the allele frequency spectrum in human 
            populations.
  - term:
      id: GO:0042802
      label: identical protein binding
    evidence_type: IPI
    original_reference_id: PMID:32296183
    review:
      summary: >-
        APIP self-interaction in binary interactome reference map.
      action: ACCEPT
      reason: >-
        Consistent with known homotetrameric structure.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "APIP/MtnB exists as a tetramer in solution"
        - reference_id: PMID:32296183
          supporting_text: Apr 8. A reference map of the human binary protein 
            interactome.
  - term:
      id: GO:0070372
      label: regulation of ERK1 and ERK2 cascade
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: >-
        Transferred from mouse ortholog. The evidence for APIP involvement in ERK1/2
        cascade regulation is weak and may not represent a core function.
      action: UNDECIDED
      reason: >-
        Unable to access primary literature for the mouse ortholog annotation to
        evaluate the strength of evidence. This may represent a peripheral or
        context-dependent effect rather than a core function.
      additional_reference_ids:
        - UniProtKB:Q9WVQ5
  - term:
      id: GO:0005737
      label: cytoplasm
    evidence_type: IDA
    original_reference_id: PMID:23285211
    review:
      summary: >-
        Direct experimental evidence for cytoplasmic localization by immunofluorescence.
        "APIP was detected mainly in the cytoplasm of HeLa cells" (PMID:23285211).
      action: ACCEPT
      reason: >-
        Strong experimental evidence for cytoplasmic localization, consistent with
        its role in the cytosolic methionine salvage pathway.
      supported_by:
        - reference_id: PMID:23285211
          supporting_text: "In accordance with its putative role in the methionine
            salvage pathway, APIP was detected mainly in the cytoplasm of HeLa cells
            by immunofluorescence"
  - term:
      id: GO:0008270
      label: zinc ion binding
    evidence_type: IDA
    original_reference_id: PMID:24367089
    review:
      summary: >-
        Crystal structure at 2.0 A resolution (PDB 4M6R) directly demonstrates zinc
        binding at the active site. His115, His117, and His195 coordinate the zinc
        ion.
      action: ACCEPT
      reason: >-
        High-resolution structural data directly demonstrates zinc binding, which
        is
        essential for catalytic activity.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "The crystal structure was determined at 2.0-Å resolution,
            revealing an overall fold similar to members of the zinc-dependent class
            II aldolase family"
  - term:
      id: GO:0043066
      label: negative regulation of apoptotic process
    evidence_type: IMP
    original_reference_id: PMID:24367089
    review:
      summary: >-
        APIP inhibits caspase-9-dependent apoptosis by binding to Apaf-1 CARD and
        competing with procaspase-9 for apoptosome formation. Importantly, "APIP/MtnB
        functions as a cell death inhibitor independently of its MtnB enzyme activity
        for apoptosis" (PMID:24367089). This is a moonlighting function.
      action: KEEP_AS_NON_CORE
      reason: >-
        This is a well-documented moonlighting function of APIP that is INDEPENDENT
        of its enzymatic activity. It represents a secondary regulatory role rather
        than the primary evolved function. The anti-apoptotic effect requires physical
        binding to Apaf-1 but not dehydratase activity.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "APIP/MtnB functions as a cell death inhibitor independently
            of its MtnB enzyme activity for apoptosis induced by either hypoxia or
            etoposide"
        - reference_id: PMID:24367089
          supporting_text: "APIP, Apaf-1 interacting protein, has been known to inhibit
            two main types of programmed cell death, apoptosis and pyroptosis"
  - term:
      id: GO:0046570
      label: methylthioribulose 1-phosphate dehydratase activity
    evidence_type: IDA
    original_reference_id: PMID:24367089
    review:
      summary: >-
        Direct enzyme assay demonstrated dehydratase activity with Km = 9.32 uM and
        Vmax = 1.39 umol/min/mg. Mutational analysis confirmed active site residues
        (Q96A, C97A, H115A, E139A affect activity).
      action: ACCEPT
      reason: >-
        This is the core molecular function of APIP, demonstrated by direct biochemical
        characterization with kinetic parameters.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "Here we report the structural and enzymatic characterization
            of human APIP as an MtnB enzyme with a Km of 9.32 μM and a Vmax of 1.39
            μmol min(-1) mg(-1)"
  - term:
      id: GO:0051289
      label: protein homotetramerization
    evidence_type: IDA
    original_reference_id: PMID:24367089
    review:
      summary: >-
        Crystal structure and solution studies demonstrate APIP forms a homotetramer
        with C4 symmetry. "APIP/MtnB exists as a tetramer in solution and exhibits
        an
        assembly with C4 symmetry in the crystal lattice" (PMID:24367089).
      action: ACCEPT
      reason: >-
        Structural evidence directly demonstrates tetrameric assembly, which is
        required for enzymatic function (active site is at subunit interface).
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "APIP/MtnB exists as a tetramer in solution and exhibits
            an assembly with C4 symmetry in the crystal lattice. The pocket-shaped
            active site is located at the end of a long cleft between two adjacent
            subunits."
  - term:
      id: GO:0070269
      label: pyroptotic inflammatory response
    evidence_type: IMP
    original_reference_id: PMID:24367089
    review:
      summary: >-
        APIP inhibits caspase-1-dependent pyroptosis. Unlike its anti-apoptotic function,
        the anti-pyroptotic activity IS dependent on enzymatic activity. Kang et al.
        showed that enzymatic mutants lose the ability to protect against pyroptosis
        but retain anti-apoptotic activity (PMID:24367089).
      action: KEEP_AS_NON_CORE
      reason: >-
        This represents a secondary regulatory function linked to the methionine salvage
        pathway. The inhibition of pyroptosis requires APIP's enzymatic activity,
        suggesting metabolic regulation of inflammation. However, this is not the
        primary function of APIP.
      supported_by:
        - reference_id: PMID:24367089
          supporting_text: "APIP/MtnB functions as a cell death inhibitor independently
            of its MtnB enzyme activity for apoptosis induced by either hypoxia or
            etoposide, but dependently for caspase-1-induced pyroptosis"
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-6804596
    review:
      summary: >-
        Reactome pathway annotation for APIP binding to the apoptosome complex
        (APAF1:CYCS). Cytosolic localization is consistent with immunofluorescence
        data (PMID:23285211).
      action: ACCEPT
      reason: >-
        Cytosolic localization is consistent with experimental evidence and with
        APIP's role in both cytosolic methionine salvage and apoptosome regulation.
      supported_by:
        - reference_id: PMID:23285211
          supporting_text: "APIP was detected mainly in the cytoplasm of HeLa cells
            by immunofluorescence"
  - term:
      id: GO:0019509
      label: L-methionine salvage from methylthioadenosine
    evidence_type: IMP
    original_reference_id: PMID:22837397
    review:
      summary: >-
        Ko et al. (2012) confirmed APIP's role in methionine salvage through growth
        assays and MTA quantitation. "The role of APIP in methionine salvage was
        confirmed by growth assays with methionine-deficient media and quantitation
        of the methionine salvage substrate, 5'-methylthioadenosine" (PMID:22837397).
      action: ACCEPT
      reason: >-
        This is the core biological process of APIP, demonstrated by functional
        mutant phenotype studies.
      supported_by:
        - reference_id: PMID:22837397
          supporting_text: "The role of APIP in methionine salvage was confirmed by
            growth assays with methionine-deficient media and quantitation of the
            methionine salvage substrate, 5'-methylthioadenosine"
  - term:
      id: GO:0019509
      label: L-methionine salvage from methylthioadenosine
    evidence_type: IMP
    original_reference_id: PMID:23285211
    review:
      summary: >-
        Mary et al. (2012) demonstrated that APIP knockdown impairs cell growth
        when methionine is replaced by MTA. "Stable knockdown of APIP specifically
        affects growth in MTA and depletes intracellular levels of methionine"
        (PMID:23285211).
      action: ACCEPT
      reason: >-
        Independent IMP evidence confirming APIP's essential role in methionine
        salvage pathway.
      supported_by:
        - reference_id: PMID:23285211
          supporting_text: "We show that APIP depletion specifically impaired the
            capacity of cells to grow"
  - term:
      id: GO:0043066
      label: negative regulation of apoptotic process
    evidence_type: IMP
    original_reference_id: PMID:22837397
    review:
      summary: >-
        Ko et al. showed that reduced APIP expression increases sensitivity to
        caspase-9-dependent cell death. "Consistent with APIP originally being
        identified as an inhibitor of caspase-9-dependent apoptosis, the same
        allele was also associated with increased sensitivity to the chemotherapeutic
        agent carboplatin" (PMID:22837397).
      action: KEEP_AS_NON_CORE
      reason: >-
        This is a moonlighting function independent of enzymatic activity. It is
        a legitimate regulatory role but not the primary evolved function of APIP.
      supported_by:
        - reference_id: PMID:22837397
          supporting_text: "Consistent with APIP originally being identified as an
            inhibitor of caspase-9-dependent apoptosis, the same allele was also associated
            with increased sensitivity to the chemotherapeutic agent carboplatin"
  - term:
      id: GO:0070372
      label: regulation of ERK1 and ERK2 cascade
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: >-
        Annotation transferred from mouse ortholog Q9WVQ5 by sequence similarity.
      action: UNDECIDED
      reason: >-
        Cannot evaluate without access to the primary evidence for the mouse
        annotation. This may represent a peripheral or context-dependent effect.
      additional_reference_ids:
        - UniProtKB:Q9WVQ5
references:
  - id: GO_REF:0000024
    title: Manual transfer of experimentally-verified manual GO annotation data 
      to orthologs by curator judgment of sequence similarity
    findings: []
  - id: GO_REF:0000033
    title: Annotation inferences using phylogenetic trees
    findings: []
  - id: GO_REF:0000043
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword 
      mapping
    findings: []
  - id: GO_REF:0000104
    title: Electronic Gene Ontology annotations created by transferring manual 
      GO annotations between related proteins based on shared sequence features
    findings: []
  - id: GO_REF:0000107
    title: Automatic transfer of experimentally verified manual GO annotation 
      data to orthologs using Ensembl Compara
    findings: []
  - id: GO_REF:0000120
    title: Combined Automated Annotation using Multiple IEA Methods
    findings: []
  - id: PMID:16189514
    title: Towards a proteome-scale map of the human protein-protein interaction
      network.
    findings: []
  - id: PMID:19060904
    title: An empirical framework for binary interactome mapping.
    findings: []
  - id: PMID:22837397
    title: Functional genetic screen of human diversity reveals that a 
      methionine salvage enzyme regulates inflammatory cell death.
    findings:
      - statement: APIP role in methionine salvage confirmed
        supporting_text: "The role of APIP in methionine salvage was confirmed by
          growth assays with methionine-deficient media and quantitation of the methionine
          salvage substrate, 5'-methylthioadenosine"
      - statement: APIP variants affect susceptibility to both pyroptosis and 
          apoptosis
        supporting_text: "Reducing expression of APIP or exogenous addition of 5'-methylthioadenosine
          increased Salmonellae-induced cell death"
      - statement: APIP inhibits caspase-1 and caspase-9 mediated cell death
        supporting_text: "Consistent with APIP originally being identified as an inhibitor
          of caspase-9-dependent apoptosis, the same allele was also associated with
          increased sensitivity to the chemotherapeutic agent carboplatin"
  - id: PMID:23285211
    title: Functional identification of APIP as human mtnB, a key enzyme in the 
      methionine salvage pathway.
    findings:
      - statement: APIP is the human MtnB enzyme
        supporting_text: "Using a bioinformatics approach, we propose that a protein
          called APIP could perform this role"
      - statement: APIP knockdown impairs growth in MTA medium
        supporting_text: "We show that APIP depletion specifically impaired the capacity
          of cells to grow"
      - statement: APIP localizes to cytoplasm
        supporting_text: "APIP was detected mainly in the cytoplasm of HeLa cells
          by immunofluorescence"
      - statement: Two isoforms exist (long and short)
        supporting_text: "Two splice isoforms are described for APIP (APIP.long and
          APIP.short)"
  - id: PMID:24367089
    title: Structural and biochemical basis for the inhibition of cell death by 
      APIP, a methionine salvage enzyme.
    findings:
      - statement: Crystal structure at 2.0 A (PDB 4M6R)
        supporting_text: "The crystal structure was determined at 2.0-Å resolution,
          revealing an overall fold similar to members of the zinc-dependent class
          II aldolase family"
      - statement: Km = 9.32 uM, Vmax = 1.39 umol/min/mg for MtnB reaction
        supporting_text: "Here we report the structural and enzymatic characterization
          of human APIP as an MtnB enzyme with a Km of 9.32 μM and a Vmax of 1.39
          μmol min(-1) mg(-1)"
      - statement: Homotetramer with C4 symmetry
        supporting_text: "APIP/MtnB exists as a tetramer in solution and exhibits
          an assembly with C4 symmetry in the crystal lattice"
      - statement: Glu139 is catalytic acid/base
        supporting_text: "We propose an enzymatic reaction mechanism involving Glu139*
          as a catalytic acid/base"
      - statement: Anti-apoptotic activity is enzyme-independent
        supporting_text: "APIP/MtnB functions as a cell death inhibitor independently
          of its MtnB enzyme activity for apoptosis induced by either hypoxia or etoposide"
      - statement: Anti-pyroptotic activity is enzyme-dependent
        supporting_text: "APIP/MtnB functions as a cell death inhibitor independently
          of its MtnB enzyme activity for apoptosis induced by either hypoxia or etoposide,
          but dependently for caspase-1-induced pyroptosis"
  - id: PMID:25416956
    title: A proteome-scale map of the human interactome network.
    findings: []
  - id: PMID:27107014
    title: An inter-species protein-protein interaction network across vast 
      evolutionary distance.
    findings: []
  - id: PMID:29892012
    title: An interactome perturbation framework prioritizes damaging missense 
      mutations for developmental disorders.
    findings: []
  - id: PMID:31515488
    title: Extensive disruption of protein interactions by genetic variants 
      across the allele frequency spectrum in human populations.
    findings: []
  - id: PMID:32296183
    title: A reference map of the human binary protein interactome.
    findings: []
  - id: PMID:32814053
    title: Interactome Mapping Provides a Network of Neurodegenerative Disease 
      Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
    findings: []
  - id: PMID:33961781
    title: Dual proteome-scale networks reveal cell-specific remodeling of the 
      human interactome.
    findings: []
  - id: Reactome:R-HSA-6804596
    title: APAF1:CYCS binds APIP
    findings: []
  - id: file:human/APIP/APIP-deep-research-falcon.md
    title: Deep research report on APIP
    findings:
      - statement: APIP competes with procaspase-9 for Apaf-1 binding
        supporting_text: "APIP competes with procaspase-9 for Apaf-1 binding, inhibiting
          apoptosome-driven caspase-9 activation and offering cytoprotection in hypoxia/ischemia
          models"
      - statement: Enzymatic activity dispensable for anti-apoptotic effects
        supporting_text: "APIP's enzymatic activity is dispensable for anti-apoptotic
          effects under hypoxia/etoposide, but required for suppression of caspase-1-dependent
          pyroptosis"
core_functions:
  - description: >-
      APIP is a zinc-dependent enzyme that catalyzes the dehydration of
      5-methylthioribulose-1-phosphate (MTRu-1-P) to 2,3-diketo-5-methylthiopentyl-1-phosphate
      in the methionine salvage pathway. This is the primary evolved function of APIP,
      supported by structural data (PDB 4M6R), enzyme kinetics (Km = 9.32 uM), and
      functional studies demonstrating that APIP knockdown impairs methionine recycling
      from MTA.
    molecular_function:
      id: GO:0046570
      label: methylthioribulose 1-phosphate dehydratase activity
    directly_involved_in:
      - id: GO:0019509
        label: L-methionine salvage from methylthioadenosine
    locations:
      - id: GO:0005829
        label: cytosol
    supported_by:
      - reference_id: PMID:24367089
        supporting_text: "Here we report the structural and enzymatic characterization
          of human APIP as an MtnB enzyme with a Km of 9.32 μM and a Vmax of 1.39
          μmol min(-1) mg(-1)"
      - reference_id: PMID:23285211
        supporting_text: "these results confirm the involvement of APIP in the methionine
          salvage pathway"
proposed_new_terms: []
suggested_questions:
  - question: >-
      What is the mechanism by which APIP's enzymatic activity regulates pyroptosis
      but not apoptosis? The differential requirement for enzymatic activity between
      anti-apoptotic (enzyme-independent) and anti-pyroptotic (enzyme-dependent)
      functions suggests distinct regulatory mechanisms.
  - question: >-
      Does APIP have additional moonlighting functions related to its numerous
      protein-protein interactions detected in high-throughput studies? APIP
      interacts with many proteins beyond Apaf-1 and caspase-1, and the functional
      significance of these interactions is unclear.
suggested_experiments: []

APIP

Gene Description

Existing Annotations Review

Core Functions

References

Suggested Questions for Experts

📚 Additional Documentation

Deep Research Falcon

Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

Target Gene/Protein Identity (from UniProt):

MANDATORY VERIFICATION STEPS:

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

Research Target:

Output

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

Target Gene/Protein Identity (from UniProt):

MANDATORY VERIFICATION STEPS:

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

Research Target:

Citations

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